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moorepants / dissertation

Source for my 2012 UCD dissertation "Human Control of a Bicycle"
http://moorepants.github.io/dissertation/
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PluginNotFound: plugin pybtex.style.formatting.alpha not found #1

Closed certik closed 12 years ago

certik commented 12 years ago

I am getting PluginNotFound: plugin pybtex.style.formatting.alpha not found, any ideas how to install it? I've installed sphinxcontrib-bibtex which installed pybtex.

Qsnake: ondrej@hawk:~/repos/dissertation(master)$ make html
sphinx-build -b html -d _build/doctrees   . _build/html
Running Sphinx v1.1
loading pickled environment... not yet created
building [html]: targets for 16 source files that are out of date
updating environment: 16 added, 0 changed, 0 removed
WARNING: could not open bibtex file /home/ondrej/repos/dissertation/data/bicycle.bib.

Exception occurred:
  File "build/bdist.linux-x86_64/egg/pybtex/plugin/__init__.py", line 161, in find_plugin
    raise PluginNotFound(plugin_group, name, filename)
PluginNotFound: plugin pybtex.style.formatting.alpha not found
The full traceback has been saved in /tmp/sphinx-err-P3XUTN.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
Either send bugs to the mailing list at <http://groups.google.com/group/sphinx-dev/>,
or report them in the tracker at <http://bitbucket.org/birkenfeld/sphinx/issues/>. Thanks!
make: *** [html] Error 1
moorepants commented 12 years ago

Yes, you will need to have these two branches from pybtex (https://code.launchpad.net/~ero-sennin/pybtex/trunk/+activereviews)

Download the latest pybtex source and then merge in these two branches:

lp:~matthias-troffaes/pybtex/label-alpha ⇒ lp:pybtex lp:~matthias-troffaes/pybtex/sorting-bugfix ⇒ lp:pybtex

moorepants commented 12 years ago

Another option is to change the :style: alpha directive option in the zreferences.rst file to :style: unsrt.

certik commented 12 years ago

I see. Since I don't use bzr, here is how to do it:

bzr branch lp:pybtex
cd pybtex
bzr merge lp:~matthias-troffaes/pybtex/label-alpha
bzr commit
bzr merge lp:~matthias-troffaes/pybtex/sorting-bugfix
bzr commit

I installed it. Now I am getting:

WARNING: could not open bibtex file /home/ondrej/repos/dissertation/data/bicycle.bib.

Exception occurred:
  File "build/bdist.linux-x86_64/egg/pybtex/style/labels/alpha.py", line 25, in <module>
ImportError: cannot import name Counter
certik commented 12 years ago

Applying the patch as you suggested:

diff --git a/zreferences.rst b/zreferences.rst
index 310c203..d6ff718 100644
--- a/zreferences.rst
+++ b/zreferences.rst
@@ -3,4 +3,4 @@ References

 .. bibliography:: data/bicycle.bib
    :encoding: latex+utf8
-   :style: alpha
+   :style: unsrt

Allows to build the html, but it is missing all references. Here is the full log: https://gist.github.com/3506923, maybe you recognize some problem there?

moorepants commented 12 years ago

I didn't include the bib file because I use a common bib file for all of my papers. I created a symlink to it in the data directory. For now the just place this bib file in the data directory (create it if it isn't there). Here it is:

https://gist.github.com/3506942

I'll think about the best way to include this. I guess I could include it as a static file in the repo.

moorepants commented 12 years ago

@certik I'm going to hit the hay (East coast time zone right now). I think the next problem you'll have is not having the figures. Check my suggestions in the README about simply downloading: http://mae.ucdavis.edu/~biosport/jkm/dissertation/dissertation-data.tar.bz2 with the pre-generated figures and such. That's the easy way to handle things right now as generating everything will take a long time.

Thanks for trying this out, I'm already realizing that I need much more work to make this build with no hiccups. I'll check back in the morning to see if you have other issues.

certik commented 12 years ago

I think you should simply commit everything needed to easily build it. It's ok that you can also generate it from sources (reproducibility).

Here is how to fix the bibtex and tables/figs issue:

wget http://mae.ucdavis.edu/~biosport/jkm/dissertation/dissertation-data.tar.bz2
tar xjf dissertation-data.tar.bz2
cd data
rm bicycle.bib
wget https://raw.github.com/gist/3506942/73904ec9abaf7f7d6b3cb40b0123bcdfe456f532/bicycle.bib

Alternatively, just post the exact instructions (copy mine above for example) into the Readme. That's enough too.

Here is my current log: https://gist.github.com/3507141, still a lot of errors. In particular, the figures are still missing. I don't know why...

moorepants commented 12 years ago

@certik I've updated the README with a build section and exact instructions. The separate download of the bicycle.bib file is not needed now and the figures and tables are now included in the dissertation-data download. I've tested the instructions in a clean virtualenv on my system and all seems to work out just fine. I think it should all work now. Thanks for your help, having someone else struggle through my mess of code is super helpful.

certik commented 12 years ago

As of 6d4425431edb1c0d2afb02c37e035eb471a0d237 and following the README I am still hitting the problem:

$ make html
[...]
Exception occurred:
  File "build/bdist.linux-x86_64/egg/pybtex/style/labels/alpha.py", line 25, in <module>
ImportError: cannot import name Counter
The full traceback has been saved in /tmp/sphinx-err-SRGTPO.log, if you want to report the issue to the developers.

Which gets resolved by the patch:

diff --git a/zreferences.rst b/zreferences.rst
index 310c203..d6ff718 100644
--- a/zreferences.rst
+++ b/zreferences.rst
@@ -3,4 +3,4 @@ References

 .. bibliography:: data/bicycle.bib
    :encoding: latex+utf8
-   :style: alpha
+   :style: unsrt

Now html builds with just the following warnings:

$ make html
sphinx-build -b html -d _build/doctrees   . _build/html
Making output directory...
Running Sphinx v1.1
loading pickled environment... not yet created
building [html]: targets for 16 source files that are out of date
updating environment: 16 added, 0 changed, 0 removed
checking for /home/ondrej/repos/dissertation/data/bicycle.bib in bibtex cache... not found
parsing bibtex file /home/ondrej/repos/dissertation/data/bicycle.bib... parsed 777 entries

/home/ondrej/repos/dissertation/README.rst:12: WARNING: Duplicate explicit target name: "web".
/home/ondrej/repos/dissertation/README.rst:12: WARNING: Duplicate explicit target name: "src".
/home/ondrej/repos/dissertation/README.rst:12: WARNING: Duplicate explicit target name: "docs".
/home/ondrej/repos/dissertation/README.rst:12: WARNING: Duplicate explicit target name: "web".
/home/ondrej/repos/dissertation/README.rst:12: WARNING: Duplicate explicit target name: "src".
/home/ondrej/repos/dissertation/README.rst:12: WARNING: Duplicate explicit target name: "docs".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "web".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "src".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "docs".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "web".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "src".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "docs".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "web".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "src".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "docs".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "web".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "src".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "docs".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "web".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "src".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "docs".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "web".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "src".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "docs".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "web".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "src".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "docs".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "web".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "src".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "docs".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "web".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "src".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "docs".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "src".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "src".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "src".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "src".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "src".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "src".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "src".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "src".
/home/ondrej/repos/dissertation/README.rst:77: WARNING: Duplicate explicit target name: "src".
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/ondrej/repos/dissertation/README.rst:: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [100%] zreferences                                            
writing additional files... genindex search
copying images... [ 10%] figures/physicalparameters/CrescendoForkTorsionalFirst2copying images... [ 13%] figures/physicalparameters/CrescendoFwheelTorsionalFirscopying images... [ 15%] figures/physicalparameters/BrowserInsForkCompoundFirst.copying images... [ 73%] figures/physicalparameters/BrowserFrameCompoundFirst2.pcopying images... [100%] figures/davisbicycle/beam.png                          
copying static files... done
dumping search index... done
dumping object inventory... done
build succeeded, 43 warnings.

Build finished. The HTML pages are in _build/html.

The latex version has about 200 warnings, here is the log:

$ make latex
sphinx-build -b latex -d _build/doctrees   . _build/latex
Making output directory...
Running Sphinx v1.1
loading pickled environment... done
building [latex]: all documents
updating environment: 0 added, 0 changed, 0 removed
looking for now-outdated files... none found
processing HumanControlofaBicycle.tex... index preface acknowledgements abstract introduction eom extensions physicalparameters parameterstudy delftbicycle motioncapture davisbicycle control systemidentification zreferences 
resolving references...
writing... /home/ondrej/repos/dissertation/eom.rst:: WARNING: unusable reference target found: _images/typical-bicycle-geometry.png
/home/ondrej/repos/dissertation/eom.rst:: WARNING: unusable reference target found: _images/bicycle-geometry.png
/home/ondrej/repos/dissertation/eom.rst:: WARNING: unusable reference target found: _images/bicycle-coordinates.png
/home/ondrej/repos/dissertation/eom.rst:: WARNING: unusable reference target found: _images/meijaard2007-figure-four.png
/home/ondrej/repos/dissertation/eom.rst:: WARNING: unusable reference target found: _images/meijaard2007-figure-four-linear.png
/home/ondrej/repos/dissertation/eom.rst:: WARNING: unusable reference target found: _images/root-locus-complex.png
/home/ondrej/repos/dissertation/eom.rst:: WARNING: unusable reference target found: _images/root-locus.png
/home/ondrej/repos/dissertation/eom.rst:: WARNING: unusable reference target found: _images/eVecHalf.png
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done
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figures/davisbicycle/roll-trailer-annotated.png figures/motioncapture/3017wheel.pdf figures/delftbicycle/instrumented-bicycle.jpg figures/davisbicycle/bump.jpg figures/eom/eVecFive.png figures/motioncapture/3017rAng.pdf figures/extensions/lorenzo-high.jpg figures/parameterstudy/head-tube-angle.png figures/motioncapture/RollAngleNb.png figures/extensions/arms-phasor-five.png figures/davisbicycle/speedometer.jpg figures/parameterstudy/bode-speeds.pdf figures/systemidentification/example-fit.pdf figures/davisbicycle/processed-data.pdf figures/motioncapture/marker-location.pdf figures/davisbicycle/knee-restraints.jpg figures/motioncapture/towing3classes.pdf figures/eom/eVecSeven.png figures/davisbicycle/steer-torque-design.png figures/physicalparameters/BrowserInsForkCompoundFirst.jpg figures/eom/root-locus.pdf figures/delftbicycle/normal-freq.png figures/davisbicycle/eaton-steer-torque.png figures/davisbicycle/roll-calibration.pdf figures/davisbicycle/beam.pdf figures/motioncapture/markers.jpg figures/eom/root-locus-complex.pdf figures/delftbicycle/treadmill.jpg figures/control/commanded-steer-torque.pdf figures/motioncapture/steer-angle-pedal.pdf figures/physicalparameters/com-triangle.pdf figures/motioncapture/YawAngleNb.png figures/extensions/rider-lean-damp-stiff.pdf figures/delftbicycle/steer-sigma.png figures/systemidentification/pavilion-lane-change.pdf figures/motioncapture/SteerAngleNb.png figures/delftbicycle/knee.jpg figures/control/inner-loops.pdf figures/davisbicycle/torque-wrench-mount.jpg figures/eom/bicycle-geometry.pdf figures/control/phiDot-locus.pdf figures/physicalparameters/batavusBrowserDim.pdf figures/davisbicycle/trailer-angle.pdf figures/systemidentification/compare-id-bode-9p0.png figures/davisbicycle/biral-steer-torque-design.png figures/parameterstudy/silver-compare.png figures/motioncapture/pedaling4classes.pdf figures/davisbicycle/bicycle-daq-gui.png figures/extensions/lat-force-impulse.pdf figures/systemidentification/a-matrix-box-plot.pdf figures/extensions/arms-phasor-three.png figures/parameterstudy/wheelbase.png figures/systemidentification/all-delta_deltac-4.png figures/motioncapture/3017bAng.pdf figures/davisbicycle/surly.jpg figures/systemidentification/A-A-Tdel-Del.pdf figures/control/commanded-lateral-human.pdf figures/davisbicycle/weir-torque-load-cell.png figures/control/phiDot-damp.pdf figures/eom/meijaard2007-figure-four-linear.pdf figures/physicalparameters/CrescendoForkTorsionalFirst2.pdf figures/delftbicycle/perturb.jpg figures/motioncapture/coef3062.pdf figures/physicalparameters/fork-offset.jpg figures/davisbicycle/bump-catcher.jpg figures/davisbicycle/steer-angle-calibration.jpg figures/physicalparameters/pendulum-angle.jpg figures/parameterstudy/cres-evec-1p5-1.png figures/physicalparameters/mass-scale.jpg figures/systemidentification/A-A-Tphi-Del.pdf figures/delftbicycle/max-amp.png figures/systemidentification/rider-id-pavilion-run.pdf 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copying TeX support files... done
build succeeded, 200 warnings.

Build finished; the LaTeX files are in _build/latex.
Run `make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically).

And finally, compiling the pdf fails with:

$ cd _build/latex/
$ make
pdflatex  'HumanControlofaBicycle.tex'
This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian)
entering extended mode
(./HumanControlofaBicycle.tex
LaTeX2e <2009/09/24>
Babel <v3.8l> and hyphenation patterns for english, usenglishmax, dumylang, noh
yphenation, loaded.
(./sphinxmanual.cls
Document Class: sphinxmanual 2009/06/02 Document class (Sphinx manual)
(/usr/share/texmf-texlive/tex/latex/base/report.cls
Document Class: report 2007/10/19 v1.4h Standard LaTeX document class
(/usr/share/texmf-texlive/tex/latex/base/size10.clo)))
[...]
LaTeX Warning: Hyper reference `physicalparameters:tabbatavusbenchmark' on page
 87 undefined on input line 5339.

LaTeX Warning: Hyper reference `physicalparameters:tabdavisbenchmark' on page 8
7 undefined on input line 5340.

)
Runaway argument?
{\textbf { Browser } & \multicolumn {2}{l|}{\textbf { Browserins } & \ETC.
! File ended while scanning use of \multicolumn.
<inserted text> 
                \par 
<*> HumanControlofaBicycle.tex

?

However, I think it's a big progress. Thanks for the help!

moorepants commented 12 years ago

I don't know why your version doesn't work with the :style: alpha option. Mine does. Are you sure you merged in both branches and have the latest development branch of sphinxcontrib.bibtex?

The latest commit fixes the html build warnings.

The warnings in the make latex command have to do with the :target: directive in the images. I set the target for images to link to the full size image so that the figures are clickable in the html output. This causes issues in the latex build though. I think they may need to be absolute urls instead of relative ones. These warnings don't really affect the latex output. I'll look into fixing them though.

I don't get the pdf build error you get. Maybe this has to do with the TeX/LaTeX version we are using. I'm using TeXLive version 2009-15.

There will be quite a few warnings in the pdf build too. I believe these are related to some upstream bugs. The hyperlinks in the pdf for the citations and footnotes do not resolve correctly. I've reported the citation issues to the sphinxcontrib.bibtex developer.